Reapr - Sampling fragment coverage - didn't get any coverage

 While running Reapr  on my genome using for the long insert libraries I received the following error.

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$ Reapr_1.0.18/reapr scaffolds.fasta LIMP_8kb_long_mapped.bam LIMP_8kb_Reapr_out perfect [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region scaffold1_size3169106:5458-6874. Already sampled 0 bases [REAPR preprocess] sampling region scaffold1_size3169106:6895-18716. Already sampled 1417 bases [REAPR preprocess] sampling region scaffold1_size3169106:30623-57811. Already sampled 13239 bases [REAPR preprocess] sampling region scaffold1_size3169106:57813-98842. Already sampled 40428 bases [REAPR preprocess] sampling region scaffold1_size3169106:98863-108371. Already sampled 81458 bases [REAPR preprocess] sampling region scaffold1_size3169106:108392-108786. Already sampled 90967 bases [REAPR preprocess] sampling region scaffold1_size3169106:108807-132036. Already sampled 91362 bases [REAPR preprocess] sampling region scaffold1_size3169106:153000-153621. Already sampled 114592 bases [REAPR preprocess] sampling region scaffold1_size3169106:153642-254312. Already sampled 115214 bases [REAPR preprocess] sampling region scaffold1_size3169106:254314-257386. Already sampled 215885 bases [REAPR preprocess] sampling region scaffold1_size3169106:257407-308464. Already sampled 218958 bases [REAPR preprocess] sampling region scaffold1_size3169106:309627-314663. Already sampled 270016 bases [REAPR preprocess] sampling region scaffold1_size3169106:314684-355810. Already sampled 275053 bases [REAPR preprocess] sampling region scaffold1_size3169106:355831-356388. Already sampled 316180 bases [REAPR preprocess] sampling region scaffold1_size3169106:356424-360553. Already sampled 316738 bases [REAPR preprocess] sampling region scaffold1_size3169106:362353-365556. Already sampled 320868 bases [REAPR preprocess] sampling region scaffold1_size3169106:365596-383718. Already sampled 324072 bases [REAPR preprocess] sampling region scaffold1_size3169106:393560-401076. Already sampled 342195 bases [REAPR preprocess] sampling region scaffold1_size3169106:401097-405358. Already sampled 349712 bases [REAPR preprocess] sampling region scaffold1_size3169106:405379-423388. Already sampled 353974 bases [REAPR preprocess] sampling region scaffold1_size3169106:423445-426298. Already sampled 371984 bases [REAPR preprocess] sampling region scaffold1_size3169106:426319-435419. Already sampled 374838 bases [REAPR preprocess] sampling region scaffold1_size3169106:435440-439265. Already sampled 383939 bases [REAPR preprocess] sampling region scaffold1_size3169106:439286-440463. Already sampled 387765 bases [REAPR preprocess] sampling region scaffold1_size3169106:440484-443034. Already sampled 388943 bases [REAPR preprocess] sampling region scaffold1_size3169106:443036-506052. Already sampled 391494 bases [REAPR preprocess] sampling region scaffold1_size3169106:506073-512313. Already sampled 454511 bases [REAPR preprocess] sampling region scaffold1_size3169106:512315-521665. Already sampled 460752 bases [REAPR preprocess] sampling region scaffold1_size3169106:526492-538394. Already sampled 470103 bases [REAPR preprocess] sampling region scaffold1_size3169106:538415-571424. Already sampled 482006 bases [REAPR preprocess] sampling region scaffold1_size3169106:571426-583083. Already sampled 515016 bases [REAPR preprocess] sampling region scaffold1_size3169106:583085-585679. Already sampled 526674 bases [REAPR preprocess] sampling region scaffold1_size3169106:585700-640937. Already sampled 529269 bases [REAPR preprocess] sampling region scaffold1_size3169106:640982-662781. Already sampled 584507 bases [REAPR preprocess] sampling region scaffold1_size3169106:662783-742983. Already sampled 606307 bases [REAPR preprocess] sampling region scaffold1_size3169106:743047-760078. Already sampled 686508 bases [REAPR preprocess] sampling region scaffold1_size3169106:765101-815949. Already sampled 703540 bases [REAPR preprocess] sampling region scaffold1_size3169106:815971-820741. Already sampled 754389 bases [REAPR preprocess] sampling region scaffold1_size3169106:820912-821293. Already sampled 759160 bases [REAPR preprocess] sampling region scaffold1_size3169106:821314-865486. Already sampled 759542 bases [REAPR preprocess] sampling region scaffold1_size3169106:865488-908573. Already sampled 803715 bases [REAPR preprocess] sampling region scaffold1_size3169106:909261-942195. Already sampled 846801 bases [REAPR preprocess] sampling region scaffold1_size3169106:942216-986026. Already sampled 879736 bases [REAPR preprocess] sampling region scaffold1_size3169106:986047-991833. Already sampled 923547 bases [REAPR preprocess] sampling region scaffold1_size3169106:991854-1003751. Already sampled 929334 bases [REAPR preprocess] sampling region scaffold1_size3169106:1003772-1027843. Already sampled 941232 bases [REAPR preprocess] sampling region scaffold1_size3169106:1029659-1034131. Already sampled 965304 bases [REAPR preprocess] sampling region scaffold1_size3169106:1034152-1034594. Already sampled 969777 bases [REAPR preprocess] sampling region scaffold1_size3169106:1034615-1057662. Already sampled 970220 bases [REAPR preprocess] sampling region scaffold1_size3169106:1057683-1063521. Already sampled 993268 bases [REAPR preprocess] sampling region scaffold1_size3169106:1063542-1064434. Already sampled 999107 bases [REAPR preprocess] Something went wrong sampling fragment coverage - didn't get any coverage. Mon Jul 18 11:42:50 SGT 2016

Solution that worked for me:

I changed the orientation of the mate pairs reads by reverse complementing before using REAPR since by default Reapr assumes that the orientation of the reads is FR. To perform RC on fastq files, I used fastx_reverse_complement. Check this page for more details.